Sat Oct 8 19:06:35 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 19:06:35 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2615 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6261652 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -31.78900 17.47300 ymin,ymax (A): -23.66700 22.97500 zmin,zma (A): -12.63100 44.22300 x,y,z range (A): 49.26200 46.64200 56.85400 scale (grids/A): 0.6261652 object centre (A): -7.158000 -0.3459997 15.79600 number of atom coordinates read : 2615 total number of charged atoms : 2475 net assigned charge : 5.500007 assigned positive charge : 395.6620 centred at (gu) : 88.47003 89.23190 90.03364 assigned negative charge : -390.1625 centred at (gu) : 88.38759 89.28578 89.89212 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6786 nv = 96 ne = 84 npr = 54400 no. pairs analyzed = 54400 no. exposed pairs = 3036 no. arc points = 21728 no. surface atoms = 1019 nbur = 1596 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 332 mr = 3835 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 175 time to turn everything in is 0.1900000 number of dielectric boundary points 3234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2141 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8226 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9827259E-09 1.6606259E-08 midg,1,midg; midg,igrid,midg 1.1418630E-08 9.6296393E-10 1,midg,midg; igrid,midg,midg -1.8490053E-09 8.5622816E-09 gauss-seidel spectral radius is 0.9867881 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 19:06:35 rms-change max change #iterations 0.1321976 19.04568 at 10iterations 1.2644211E-02 2.300133 at 20iterations 1.1935784E-03 0.1777458 at 30iterations 1.1130569E-04 1.5762329E-02 at 40iterations 1.0753050E-05 1.6417503E-03 at 50iterations finished qdiffx linear iterations at : 19:06:38 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 1.0753050E-05 1.6417503E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 19:06:39 3.620u 0.212s 0:04.11 93.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 19:06:39 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2615 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.878496 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -31.78900 17.47300 ymin,ymax (A): -23.66700 22.97500 zmin,zma (A): -12.63100 44.22300 x,y,z range (A): 49.26200 46.64200 56.85400 scale (grids/A): 1.878496 object centre (A): -7.158000 -0.3459997 15.79600 number of atom coordinates read : 2615 total number of charged atoms : 2475 net assigned charge : 5.500007 assigned positive charge : 395.6620 centred at (gu) : 85.40963 87.69523 90.10031 assigned negative charge : -390.1625 centred at (gu) : 85.16267 87.85703 89.67608 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21728 grid for indexing accessible points = 1.400000 m= 26312 mr = 51679 m= 4039 mr = 19749 m= 254 mr = 2607 m= 5 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 7080 time to turn everything in is 0.3700000 number of dielectric boundary points 29938 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 19453 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6261652 object centre at (A) : -7.158000 -0.3459997 15.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6101135E-02 4.1818105E-02 midg,1,midg; midg,igrid,midg 1.0676905E-02 -2.5900433E-04 1,midg,midg; igrid,midg,midg 2.0333501E-03 3.6388919E-02 gauss-seidel spectral radius is 0.9985962 estimated iterations to convergence 212 setup time was (sec) 0.6000000 now iterating at: 19:06:40 rms-change max change #iterations 4.125923 171.3522 at 10iterations 1.910280 68.64140 at 20iterations 0.8833486 27.13050 at 30iterations 0.4095903 12.67248 at 40iterations 0.1904008 6.039483 at 50iterations 8.8327318E-02 2.940504 at 60iterations 4.0795494E-02 1.351706 at 70iterations 1.8900316E-02 0.5871334 at 80iterations 8.7619880E-03 0.2604847 at 90iterations 4.0598926E-03 0.1245923 at 100iterations 1.8857724E-03 5.7697296E-02 at 110iterations 8.7593932E-04 2.9422760E-02 at 120iterations finished qdiffx linear iterations at : 19:06:47 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 8.7593932E-04 2.9422760E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 19:06:47 8.120u 0.211s 0:08.69 95.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 19:06:47 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2615 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.817744 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -31.78900 17.47300 ymin,ymax (A): -23.66700 22.97500 zmin,zma (A): -12.63100 44.22300 x,y,z range (A): 49.26200 46.64200 56.85400 scale (grids/A): 2.817744 object centre (A): -7.158000 -0.3459997 15.79600 number of atom coordinates read : 2615 total number of charged atoms : 2475 net assigned charge : 5.500007 assigned positive charge : 395.6620 centred at (gu) : 83.11430 86.54269 90.15043 assigned negative charge : -390.1625 centred at (gu) : 82.74408 86.78543 89.51396 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 169747 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21728 grid for indexing accessible points = 1.400000 m= 85878 mr = 124424 m= 30412 mr = 71377 m= 7204 mr = 24701 m= 1129 mr = 5554 m= 51 mr = 810 m= 0 mr = 18 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 24475 time to turn everything in is 0.9300000 number of dielectric boundary points 67537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 19797 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.878496 object centre at (A) : -7.158000 -0.3459997 15.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5295534E-02 0.4495950 midg,1,midg; midg,igrid,midg 0.1145627 -1.7022464E-02 1,midg,midg; igrid,midg,midg 3.2283295E-02 0.4516807 gauss-seidel spectral radius is 0.9992411 estimated iterations to convergence 287 setup time was (sec) 1.190000 now iterating at: 19:06:49 rms-change max change #iterations 9.665473 294.2560 at 10iterations 5.560786 122.9653 at 20iterations 3.181681 70.22298 at 30iterations 1.824325 39.16452 at 40iterations 1.040953 19.50846 at 50iterations 0.5941799 12.78651 at 60iterations 0.3389535 6.127099 at 70iterations 0.1934220 4.107031 at 80iterations 0.1104818 2.112467 at 90iterations 6.2921047E-02 1.136247 at 100iterations 3.5891697E-02 0.7101440 at 110iterations 2.0400615E-02 0.3985405 at 120iterations 1.1639241E-02 0.2052422 at 130iterations 6.6412678E-03 0.1253953 at 140iterations 3.7842719E-03 7.2599411E-02 at 150iterations 2.1606570E-03 4.0299654E-02 at 160iterations 1.2311435E-03 2.1682739E-02 at 170iterations 7.0176320E-04 1.2981415E-02 at 180iterations finished qdiffx linear iterations at : 19:07:01 total time elapsed so far: 13.11000 # loops : 180 mean,max change (kT/e) : 7.0176320E-04 1.2981415E-02 energy calculations done at 13.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 19:07:01 13.245u 0.228s 0:13.75 97.8% 0+0k 0+0io 0pf+0w